Microarray Probe Coverage

Phalanx Biotech Whole Genome Annotation Pipeline

In an effort to investigate how to generate a more complete probe set, a probe annotation pipeline has been developed using the whole genome as a reference set. Analysis of available human gene expression microarrays indicates increased probe density does not correlate with increased gene coverage or interrogation power.


Figure 1: Overview of the annotation pipeline.


OneArray® Interrogation Power




Figure 2: Probe Set Breakdown




Figure 3: Interrogation Power

The annotation pipeline was used to evaluate probe sets from several different sources. Probes were assigned to six different categories based on their alignment to the whole genome.



Table 1: Annotation criteria

The break down for the probe sets investigated (Figure 2) indicates sets with high probe density have a large amount of probe space dedicated to intergenic material (orange).

Further analysis indicates a high level of redundancy in gene coverage (Figure 3). High probe density does not correlate with good gene coverage.